This repository contains all the materials for the Simulation of Biomolecules Advanced course, part of the CCP5 Summer School taking place on July 25-27th 2023 at Durham University.
- Dr Agnieszka Bronowska, Newcastle University (AB)
- Dr Matteo Degiacomi, Durham University (MTD)
- Dr Antonia Mey, University of Edinburgh (AM)
Durham University
Room: CC0007 Computer Classroom in the Chemistry Courtyard Building
Wed: 2-3 pm CG91 For a one hour lecture
L1-8: Lectures. P: practical.
| 25th July | Session | Materials |
|---|---|---|
| 9:00-10:00 | L1: Introduction to Proteins (MTD) | Lecture Slides |
| 10:00-11:00 | L2 & P: Protein Preparation (AM) | Lecture Slides, Webserver |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L3: Introduction to Docking (AB) | Lecture Slides |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:30 | P: Docking (AB) | Practical Slides |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | P: Docking (AB) | Practical Slides |
| 26th July | Session | Materials |
|---|---|---|
| 9:00-10:00 | L4: Simulation Best Practices (AM) | Lecture Slides |
| 10:00-11:00 | P: Simulation setup with BioSimSpace (AM) | Practical Notebook |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L5 & P: Analysis Tools (AM) | Lecture Slides,  |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:00 | L6: Dimensionality Reduction & Clustering (MTD) | Lecture Slides |
| 15:00-15:30 | Coffee | ☕ |
| 15:30-17:00 | P: Dimensionality Reduction & Clustering (MTD/AM) | |
| 27th July | Session | Materials |
|---|---|---|
| 9:00-10:00 | L7: Data Classification (MTD) | Lecture Slides |
| 10:00-11:00 | P: Data Classification (MTD/AM) | |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L8: Markov State Modelling (AM) | Lecture Slides |
| 12:30-14:00 | Lunch | 🍝 |
Instructions for setting up your environment to run this workshop locally
are provided in INSTALL.md.
A full list of the required Python packages can be seen inside environment.yml.
As downloading and installing everything will take a little while, ideally you should follow these steps before the workshop starts. If you encounter any issues during installation, we can help!
If for any reason you cannot set up a local environment with all required packages, you can use Google Colab to run all workshop notebooks directly from your browser, no installation required.
BioSimSpace setup for 3_Simulation_setup
Information for the installation of this can be found in this README
The course assumes that attendees have a working knowledge of Jupyter notebooks, Python (especially the NumPy library), and the bash shell.
The BioSimSpace material in folder 3_* licenced under GPL v3.
The MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.
The MDAnalysis material in folder 4_* is licenced under CC-BY 4.0
Material in folders 1_*, 5_*, 6_*, and 7_* is licenced under CC-BY-SA 4.0.
Please see AUTHORS.md for a list of contributors to the workshop
materials.